Well, I think we need to keep in mind that a good deal of time has passed between Rise of the Horde and Beyond the Dark Portal. If Ner'zhul is presented as more of a typical "good guy" in Rise of the Horde, the subsequent years may have made him a lot more cynical. With the Frostwolves banished, Doomhammer defeated, and new bouts of civil war breaking out among the clans still on Draenor, it's easy to see how he could have abandoned past ideological convictions; he may have thought that his people were beyond saving entirely. Around the same time, he realized that with Gul'dan dead, Kil'jaeden would come after him, and decided "fuck this, I'm gonna save myself."

At least, that's my take on it.

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Many thanks to handclaw for his amazing rendition of Kargath Bladefist, which is now my avatar.